11 replies to this topic

[cardosopedro]

Hi!

I want to characterize a protein (actually, two similar proteins) by a bioinformatics approach. Therefore, I decided to create this thread so me and other people can give suggestions on "what bioinformatics tools can I use to predict function, philogeny, domain organization, ... of my protein?"

Maybe this is a too broad thread, but hopefully it will give ideas to other users.


Thanks.

[cardosopedro]

Until now I've made global alignments and domain-specific alignments for my proteins vs other homologues. I also did a table of identity/similarity. I am now constructing a neighbor-joining tree.


Other tools that I intend to use:
- predict secondary structure
- predict subcellular localization
- compare my two proteins by dot plots


Please add suggestions.
Thanks.

[pDNA]

i use the CLC Main Workbench ...a real valuable tool for such tasks ...but you have to buy it!

Regards,
p

[HomeBrew]

Look for conserved domains or motifs with NCBI's Conserved Domain Database or Sanger's Pfam database.

[cardosopedro]

HomeBrew, on 17 October 2010 - 04:23 AM, said:

Look for conserved domains or motifs with NCBI's Conserved Domain Database or Sanger's Pfam database.

Thanks for the replies.

I am also calculating evolutionary distances together with my neighbor-joining tree. I will do a search about how to interpretate those evolutionary distances though.

More suggestions?

[HomeBrew]

cardosopedro, on 17 October 2010 - 06:26 AM, said:

I am also calculating evolutionary distances together with my neighbor-joining tree. I will do a search about how to interpretate those evolutionary distances though.

There is no evolutionary information in protein sequences because proteins do not evolve -- evolution occurs at the DNA level.

[cardosopedro]

HomeBrew, on 17 October 2010 - 01:06 PM, said:

cardosopedro, on 17 October 2010 - 06:26 AM, said:

I am also calculating evolutionary distances together with my neighbor-joining tree. I will do a search about how to interpretate those evolutionary distances though.

There is no evolutionary information in protein sequences because proteins do not evolve -- evolution occurs at the DNA level.

Thank you for the info. So I think it's better to forget those evolutionary distances values... maybe I'll do it for the DNA sequences.

[cardosopedro]

Hey.

Any other suggestions?

[cardosopedro]

cardosopedro, on 20 October 2010 - 07:52 AM, said:

Hey.

Any other suggestions?

I had no success with the dot plots for comparing my two proteins. However, I did an alignment with both and found differences in the N- and C-terminal portion.

I also predicted their MW and pI. Also, I am looking for motifs in InterProScan.


Please suggest more tools if you like.

[Raviraj]

Dear all,
I am analyzing gene called ROCK1 ( accession no-NM 031098). I have to find out whether ROCK1 has any binding sites in the HES/HERP  or any sites on Notch-1 (all the experiments have done on Rat). I have found the higher expression of ROCK1 down regulates the Notch1 or vise versa in protein and RNA level. To further investigate, I need to explain through finding of binding sites in Notch-1 or HES/HERP. I am quite new to the Bioinformatics field. Could anyone can help on this?

Thanks in advance,

Ravi

[cardosopedro]

Raviraj, on 09 January 2011 - 10:11 PM, said:

Dear all,
I am analyzing gene called ROCK1 ( accession no-NM 031098). I have to find out whether ROCK1 has any binding sites in the HES/HERP  or any sites on Notch-1 (all the experiments have done on Rat). I have found the higher expression of ROCK1 down regulates the Notch1 or vise versa in protein and RNA level. To further investigate, I need to explain through finding of binding sites in Notch-1 or HES/HERP. I am quite new to the Bioinformatics field. Could anyone can help on this?

Thanks in advance,

Ravi

First I would try to find if there is a consensus binding site for ROCK1 (look in the literature). Then I would look for that motif in the two target proteins.

[Raviraj]

[/quote]

First I would try to find if there is a consensus binding site for ROCK1 (look in the literature). Then I would look for that motif in the two target proteins.
[/quote]


Thanks. I am waiting for your reply. Once you found, could you please explain to me.